In outbreak settings or persistent infections, whole-gene or whole-genome sequencing is increasingly used to demonstrate clonal spread and to identify resistance-associated alleles that may affect local empiric therapy recommendations. When ERG11-linked fluconazole resistance is present in invasive disease, echinocandins (caspofungin, micafungin, anidulafungin) are preferred first-line agents because their mechanism bypasses the Erg11 target. (OUP Academic)
Amphotericin B (and lipid formulations) remains an option for severe, refractory infections or in regions with high echinocandin resistance, though toxicity and resource constraints limit its use.

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